56 results
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2. Ten simple rules for reading a scientific paper
- Author
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William A. Petri, Kevin L Steiner, and Maureen A. Carey
- Subjects
Science and Technology Workforce ,Economics ,Social Sciences ,Scientific literature ,Careers in Research ,Key (music) ,Habits ,Learning and Memory ,Sociology ,Reading (process) ,Psychology ,Biology (General) ,media_common ,Simple (philosophy) ,Textbooks ,Ecology ,Library card ,Careers ,Publications ,Research Assessment ,Professions ,Editorial ,Computational Theory and Mathematics ,Modeling and Simulation ,Research Reporting Guidelines ,Educational Status ,Periodicals as Topic ,Employment ,QH301-705.5 ,Science Policy ,media_common.quotation_subject ,Research and Analysis Methods ,Education ,Cellular and Molecular Neuroscience ,Level of Effort ,Human Learning ,Genetics ,Mathematics education ,Learning ,Early career ,Molecular Biology ,Ecology, Evolution, Behavior and Systematics ,Publishing ,Behavior ,Research ,Cognitive Psychology ,Biology and Life Sciences ,Advice (programming) ,Reading ,Labor Economics ,People and Places ,Scientists ,Cognitive Science ,Population Groupings ,Undergraduates ,Neuroscience - Abstract
“There is no problem that a library card can't solve” according to author Eleanor Brown [1]. This advice is sound, probably for both life and science, but even the best tool (like the library) is most effective when accompanied by instructions and a basic understanding of how and when to use it. For many budding scientists, the first day in a new lab setting often involves a stack of papers, an email full of links to pertinent articles, or some promise of a richer understanding so long as one reads enough of the scientific literature. However, the purpose and approach to reading a scientific article is unlike that of reading a news story, novel, or even a textbook and can initially seem unapproachable. Having good habits for reading scientific literature is key to setting oneself up for success, identifying new research questions, and filling in the gaps in one’s current understanding; developing these good habits is the first crucial step. Advice typically centers around two main tips: read actively and read often. However, active reading, or reading with an intent to understand, is both a learned skill and a level of effort. Although there is no one best way to do this, we present 10 simple rules, relevant to novices and seasoned scientists alike, to teach our strategy for active reading based on our experience as readers and as mentors of undergraduate and graduate researchers, medical students, fellows, and early career faculty. Rules 1–5 are big picture recommendations. Rules 6–8 relate to philosophy of reading. Rules 9–10 guide the “now what?” questions one should ask after reading and how to integrate what was learned into one’s own science.
- Published
- 2020
3. Ten simple rules for developing good reading habits during graduate school and beyond.
- Author
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Méndez, Marcos
- Subjects
READING ,HABIT formation ,COMPREHENSION ,HISTORY ,PERIODICALS ,BIBLIOGRAPHICAL citations - Abstract
The author talks about several rules that a person can follow to develop good reading habits in graduate school and beyond. Topics discussed include the importance of developing the habit of reading on a daily basis; the need to develop comprehension skills; and the need to study the history of one's discipline. Also mentioned are the importance of creating a list of relevant journals, the need to read books, and the benefits of using a reference manager.
- Published
- 2018
- Full Text
- View/download PDF
4. Ten Simple Rules for a Bioinformatics Journal Club.
- Author
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Lonsdale, Andrew, Sietsma Penington, Jocelyn, Rice, Timothy, Walker, Michael, and Dashnow, Harriet
- Subjects
BIOINFORMATICS ,INFORMATION science ,COMPUTATIONAL biology ,CLUBS ,SCIENTIFIC literature ,SOCIETIES - Abstract
The article outlines the rules for a bioinformatics journal club which, according to the authors, is a great way to take in the scientific literature, keep up with developments in their field, and hone their communication and analytical skills. The rules include holding a journal club at eight in the morning, finding good articles for discussion, and expanding the roster of leaders as people join the journal club.
- Published
- 2016
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5. Ten simple rules for measuring the impact of workshops.
- Author
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Sufi, Shoaib, Nenadic, Aleksandra, Silva, Raniere, Balzano, Melissa, Coelho, Sara, Ford, Heather, Jones, Catherine, Higgins, Vanessa, Duckles, Beth, Simera, Iveta, de Beyer, Jennifer A., Struthers, Caroline, Nurmikko-Fuller, Terhi, Bellis, Louisa, Miah, Wadud, Wilde, Adriana, Emsley, Iain, and Philippe, Olivier
- Subjects
FORUMS ,RESEARCH ,DECISION making ,STRATEGIC planning ,PARTICIPATION - Abstract
Workshops are used to explore a specific topic, to transfer knowledge, to solve identified problems, or to create something new. In funded research projects and other research endeavours, workshops are the mechanism used to gather the wider project, community, or interested people together around a particular topic. However, natural questions arise: how do we measure the impact of these workshops? Do we know whether they are meeting the goals and objectives we set for them? What indicators should we use? In response to these questions, this paper will outline rules that will improve the measurement of the impact of workshops. [ABSTRACT FROM AUTHOR]
- Published
- 2018
- Full Text
- View/download PDF
6. Systems Approaches to the Eukaryotic Stress Response.
- Author
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Vogel, Christine
- Subjects
PHYSIOLOGICAL stress ,EUKARYOTES ,PROTEIN expression ,PROJECT management ,MOTIVATION (Psychology) ,RESEARCH personnel - Abstract
The author discusses aspects of her career and system approaches to stress response in eukaryotes. Topics include protein expression associated to environmental stress, project management, and motivation for laboratory members. In addition, she also presents advice to beginning researchers and principal investigators (PIs).
- Published
- 2016
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7. k-OptForce: Integrating Kinetics with Flux Balance Analysis for Strain Design.
- Author
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Chowdhury, Anupam, Zomorrodi, Ali R., and Maranas, Costas D.
- Subjects
DYNAMICS ,COMPUTER network protocols ,BIOCHEMICAL engineering ,MICROORGANISMS ,METABOLITES - Abstract
Computational strain design protocols aim at the system-wide identification of intervention strategies for the enhanced production of biochemicals in microorganisms. Existing approaches relying solely on stoichiometry and rudimentary constraint-based regulation overlook the effects of metabolite concentrations and substrate-level enzyme regulation while identifying metabolic interventions. In this paper, we introduce k-OptForce, which integrates the available kinetic descriptions of metabolic steps with stoichiometric models to sharpen the prediction of intervention strategies for improving the bio-production of a chemical of interest. It enables identification of a minimal set of interventions comprised of both enzymatic parameter changes (for reactions with available kinetics) and reaction flux changes (for reactions with only stoichiometric information). Application of k-OptForce to the overproduction of L-serine in E. coli and triacetic acid lactone (TAL) in S. cerevisiae revealed that the identified interventions tend to cause less dramatic rearrangements of the flux distribution so as not to violate concentration bounds. In some cases the incorporation of kinetic information leads to the need for additional interventions as kinetic expressions render stoichiometry-only derived interventions infeasible by violating concentration bounds, whereas in other cases the kinetic expressions impart flux changes that favor the overproduction of the target product thereby requiring fewer direct interventions. A sensitivity analysis on metabolite concentrations shows that the required number of interventions can be significantly affected by changing the imposed bounds on metabolite concentrations. Furthermore, k-OptForce was capable of finding non-intuitive interventions aiming at alleviating the substrate-level inhibition of key enzymes in order to enhance the flux towards the product of interest, which cannot be captured by stoichiometry-alone analysis. This study paves the way for the integrated analysis of kinetic and stoichiometric models and enables elucidating system-wide metabolic interventions while capturing regulatory and kinetic effects. [ABSTRACT FROM AUTHOR]
- Published
- 2014
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8. Ten simple rules for giving an effective academic job talk.
- Author
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Sura, Shayna A., Smith, Lauren L., Ambrose, Monique R., Amorim, C. Eduardo Guerra, Beichman, Annabel C., Gomez, Ana C. R., Juhn, Mark, Kandlikar, Gaurav S., Miller, Julie S., Mooney, Jazlyn, Mummah, Riley O., Lohmueller, Kirk E., and Lloyd-Smith, James O.
- Subjects
JOB applications ,CAREER development ,EMPLOYMENT interviewing ,CONVERSATION ,RESEARCH grants ,JOB hunting - Published
- 2019
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9. Ten simple rules when considering retirement.
- Author
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Bourne, Philip E.
- Subjects
RETIREMENT ,COMPUTATIONAL biology ,BIOCOMPATIBILITY ,STEM education ,AUTOBIOGRAPHY - Abstract
The article presents author's comments on the rules that should be considered during retirement. It focuses on the retirement in computational biology. It offers information on autobiographical perspective on biomedical data. It focuses on the need for expertise in science, technology, engineering, and medicine (STEM).
- Published
- 2018
- Full Text
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10. Ten simple rules for writing a popular science book.
- Author
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Kucharski, Adam J.
- Subjects
AUTHORSHIP ,AUTHORS ,AUTHOR-reader relationships ,BOOKS ,WRITING - Abstract
The article focuses on main points to be considered by a budding author while writing a book. It is advised to write a complete draft, put it in a drawer, then forget about it while writing a good novel. It is recommended to find the right topic for the book and it is better if the topic is timely and new.
- Published
- 2018
- Full Text
- View/download PDF
11. Ten simple rules for successfully completing a graduate degree in Latin America.
- Author
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Ruelas Inzunza, Ernesto, Salazar-Rivera, Gabriela I., Láinez, Magdiel, Ruiz-Gómez, María Guadalupe, Domínguez-Eusebio, Carlo A., Cristóbal-Sánchez, Griselda, Teodosio Faustino, Issaac A., Pérez-López, Edel, Campbell, Meagan L., Merfa, Marcus Vinicius, Latorre Beltrán, Ivonne Tatiana, Armas, Fernanda, and Mota-Vargas, Claudio
- Subjects
GRADUATE education ,LIFE science education ,LIFE sciences ,SCHOLARSHIPS ,EDUCATION - Abstract
This article offers tips for students to complete a graduate degree in biological sciences in Latin America. Topics discussed include the features that underlie the performance of graduate programs around the world, the importance of investigating the graduate program and the adviser, scholarship programs for graduate students, and the need to follow administrative procedures from admission to graduation.
- Published
- 2017
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12. Ten simple rules for getting the most out of a summer laboratory internship.
- Author
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Aicher, Toby P., Barabási, Dániel L., Harris, Benjamin D., Nadig, Ajay, and Williams, Kaitlin L.
- Subjects
INTERNSHIP programs ,LEARNING ,COMMUNICATION ,MENTORS ,SOCIAL interaction - Abstract
The author offers rules for getting the most out of a summer laboratory internship. The rules discussed include summer internships afford no such luxury which is important to optimize learning by working diligently and efficiently, productive stream of communication with mentor and internship has a programming course which can start learning computational skills. It mentions satisfying project, a supportive group, and unique social interactions.
- Published
- 2017
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13. Ten simple rules for providing optimal administrative support to research teams.
- Author
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Garrido, Romina, Trowbridge, Casandra A., and Tamura, Nana
- Subjects
RESEARCH teams ,ADMINISTRATIVE assistants ,SOCIAL learning ,PROFESSIONAL relationships ,SCIENTIFIC community ,CULTURAL pluralism ,HEBBIAN memory ,BUSINESS communication - Abstract
You can help your principal investigator on the oversight of grant rules and procedures, keeping protocols up to date, writing reports, and fulfilling requests from the Institutional Review Board (IRB). Regardless, what is important is for the administrator to be curious about science and make the effort to get a basic familiarity with the scientific discipline and academic working environment they are supporting. Although human resources, principal investigators, and lab managers are a large part of the onboarding process for a new employee, administrative staff are typically involved in the process as well. [Extracted from the article]
- Published
- 2019
- Full Text
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14. Ten simple rules for helping newcomers become contributors to open projects.
- Author
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Sholler, Dan, Steinmacher, Igor, Ford, Denae, Averick, Mara, Hoye, Mike, and Wilson, Greg
- Subjects
SOCIAL learning ,OPEN source software ,SCIENCE education ,HEBBIAN memory ,SOFTWARE engineering ,LIFE sciences ,SCIENCE & state ,HUMAN-computer interaction - Abstract
Open-source software projects are also communities of effort. "...developers who join an organization through these programs are half as likely to transition into long-term community members than developers who do not use these programs... although developers who do succeed through these programs find them valuable". 47 Fagerholm F, Guinea AS, Münch J, Borenstein J. The role of mentoring and project characteristics for onboarding in open source software projects. [Extracted from the article]
- Published
- 2019
- Full Text
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15. Network trade-offs and homeostasis in Arabidopsis shoot architectures.
- Author
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Conn, Adam, Chandrasekhar, Arjun, Rongen, Martin van, Leyser, Ottoline, Chory, Joanne, and Navlakha, Saket
- Subjects
COMPUTER architecture ,HOMEOSTASIS ,PLANT shoots ,PLANT selection ,BOTANY ,PLANT anatomy - Abstract
Understanding the optimization objectives that shape shoot architectures remains a critical problem in plant biology. Here, we performed 3D scanning of 152 Arabidopsis shoot architectures, including wildtype and 10 mutant strains, and we uncovered a design principle that describes how architectures make trade-offs between competing objectives. First, we used graph-theoretic analysis to show that Arabidopsis shoot architectures strike a Pareto optimal that can be captured as maximizing performance in transporting nutrients and minimizing costs in building the architecture. Second, we identify small sets of genes that can be mutated to shift the weight prioritizing one objective over the other. Third, we show that this prioritization weight feature is significantly less variable across replicates of the same genotype compared to other common plant traits (e.g., number of rosette leaves, total volume occupied). This suggests that this feature is a robust descriptor of a genotype, and that local variability in structure may be compensated for globally in a homeostatic manner. Overall, our work provides a framework to understand optimization trade-offs made by shoot architectures and provides evidence that these trade-offs can be modified genetically, which may aid plant breeding and selection efforts. [ABSTRACT FROM AUTHOR]
- Published
- 2019
- Full Text
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16. From trainees to trainers to instructors: Sustainably building a national capacity in bioinformatics training.
- Author
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McGrath, Annette, Champ, Katherine, Shang, Catherine A., van Dam, Ellen, Brooksbank, Cath, and Morgan, Sarah L.
- Subjects
LEAD ,TRAINING planes ,TRAINING of scientists ,MOLECULAR biology ,INDUSTRIAL research ,BIOINFORMATICS - Abstract
Demand for training life scientists in bioinformatics skills led to the development of a train-the-trainer collaboration between the European Molecular Biology Laboratory–European Bioinformatics Institute (EMBL-EBI) and 2 Australian organisations, Bioplatforms Australia and Commonwealth Scientific and Industrial Research Organisation (CSIRO) in 2012. The goal of the collaboration was to establish a group of trained instructors who could develop and deliver short bioinformatics courses nationally. A train-the-trainer course introduces instructors to aspects of andragogy and evidence-based learning principles to help them better design, develop, and deliver high-quality training. Since then, both the number of trainers in the network and the course portfolio have grown. Best practises have been developed and shared between the Australian cohort and EMBL-EBI to address common challenges in bioinformatics training. The Australian trainer cohort undertook a train-the-trainer instructor course, again with EMBL-EBI, and subsequently successfully delivered train-the-trainer courses to interested bioinformatics trainers within Australia. We conclude that a train-the-trainer approach can help build national capacity and maintain a critical mass of trained instructors. [ABSTRACT FROM AUTHOR]
- Published
- 2019
- Full Text
- View/download PDF
17. Efficient algorithms to discover alterations with complementary functional association in cancer.
- Author
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Sarto Basso, Rebecca, Hochbaum, Dorit S., and Vandin, Fabio
- Subjects
CANCER genetics ,PERTURBATION theory ,PHENOTYPES ,ALGORITHMS ,COMPUTATIONAL biology - Abstract
Recent large cancer studies have measured somatic alterations in an unprecedented number of tumours. These large datasets allow the identification of cancer-related sets of genetic alterations by identifying relevant combinatorial patterns. Among such patterns, mutual exclusivity has been employed by several recent methods that have shown its effectiveness in characterizing gene sets associated to cancer. Mutual exclusivity arises because of the complementarity, at the functional level, of alterations in genes which are part of a group (e.g., a pathway) performing a given function. The availability of quantitative target profiles, from genetic perturbations or from clinical phenotypes, provides additional information that can be leveraged to improve the identification of cancer related gene sets by discovering groups with complementary functional associations with such targets. In this work we study the problem of finding groups of mutually exclusive alterations associated with a quantitative (functional) target. We propose a combinatorial formulation for the problem, and prove that the associated computational problem is computationally hard. We design two algorithms to solve the problem and implement them in our tool UNCOVER. We provide analytic evidence of the effectiveness of UNCOVER in finding high-quality solutions and show experimentally that UNCOVER finds sets of alterations significantly associated with functional targets in a variety of scenarios. In particular, we show that our algorithms find sets which are better than the ones obtained by the state-of-the-art method, even when sets are evaluated using the statistical score employed by the latter. In addition, our algorithms are much faster than the state-of-the-art, allowing the analysis of large datasets of thousands of target profiles from cancer cell lines. We show that on two such datasets, one from project Achilles and one from the Genomics of Drug Sensitivity in Cancer project, UNCOVER identifies several significant gene sets with complementary functional associations with targets. Software available at: . [ABSTRACT FROM AUTHOR]
- Published
- 2019
- Full Text
- View/download PDF
18. Ten simple rules for providing a meaningful research experience to high school students.
- Author
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Lescak, Emily A., O’Neill, Kate M., Collu, Giovanna M., and Das, Subhamoy
- Subjects
RESEARCH ,HIGH school students ,MENTORING ,STEM education ,STEM occupations - Abstract
An editorial is presented on rules for providing a meaningful research experience to high school students. Topics discussed include ten rules for becoming an effective research mentor for high school students and their training, research opportunities as undergraduates and career consideration in science, technology, engineering, and mathematics and bridging the gap between scientists and the general public on scientific research.
- Published
- 2019
- Full Text
- View/download PDF
19. Ten simple rules towards healthier research labs.
- Author
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Maestre, Fernando T.
- Subjects
SCHOLARS ,HEALTH ,PRIVATE investigators ,SCIENTISTS ,SCIENCE - Abstract
The negative effects of extremely competitive academic and research environments on the performance and health of researchers are well known and common worldwide. The prevalence of these effects, particularly among early career researchers, calls for a more humane and people-centered way of working within research labs. Although there is growing concern about the urgent need for a better life–work balance when doing science, there are not many examples about how this could be achieved in practice. In this article, I introduce 10 simple rules to make the working environment of research labs more nurturing, collaborative, and people-centered. These rules are directed towards existing and future principal investigators (PIs) but will be of interest to anyone working in a research lab and/or dealing with how to improve working conditions for scientists. [ABSTRACT FROM AUTHOR]
- Published
- 2019
- Full Text
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20. Contextual influence on confidence judgments in human reinforcement learning.
- Author
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Lebreton, Maël, Bacily, Karin, Palminteri, Stefano, and Engelmann, Jan B.
- Subjects
REINFORCEMENT learning ,DECISION making ,CONFIDENCE ,LEARNING strategies ,DISCOVERY method (Teaching) - Abstract
The ability to correctly estimate the probability of one’s choices being correct is fundamental to optimally re-evaluate previous choices or to arbitrate between different decision strategies. Experimental evidence nonetheless suggests that this metacognitive process—confidence judgment- is susceptible to numerous biases. Here, we investigate the effect of outcome valence (gains or losses) on confidence while participants learned stimulus-outcome associations by trial-and-error. In two experiments, participants were more confident in their choices when learning to seek gains compared to avoiding losses, despite equal difficulty and performance between those two contexts. Computational modelling revealed that this bias is driven by the context-value, a dynamically updated estimate of the average expected-value of choice options, necessary to explain equal performance in the gain and loss domain. The biasing effect of context-value on confidence, revealed here for the first time in a reinforcement-learning context, is therefore domain-general, with likely important functional consequences. We show that one such consequence emerges in volatile environments, where the (in)flexibility of individuals’ learning strategies differs when outcomes are framed as gains or losses. Despite apparent similar behavior- profound asymmetries might therefore exist between learning to avoid losses and learning to seek gains. [ABSTRACT FROM AUTHOR]
- Published
- 2019
- Full Text
- View/download PDF
21. Ten simple rules for organizing a webinar series.
- Author
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Fadlelmola, Faisal M., Panji, Sumir, Ahmed, Azza E., Ghouila, Amel, Akurugu, Wisdom A., Entfellner, Jean-Baka Domelevo, Souiai, Oussema, Mulder, Nicola, and null, null
- Subjects
WEBINARS ,COMMUNITIES ,AUDIENCES ,EMAIL ,SOCIAL media - Abstract
The article presents ten simple rules for hosting a regular webinar series with particular emphasis on resource-constrained communities like many in Africa. Topics include aligning a webinar theme to the expectations of the audience; settling on a convenient and user friendly webinar platform; and announcing webinars through mailing lists and social media platform.
- Published
- 2019
- Full Text
- View/download PDF
22. A Pareto approach to resolve the conflict between information gain and experimental costs: Multiple-criteria design of carbon labeling experiments.
- Author
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Nöh, Katharina, Niedenführ, Sebastian, Beyß, Martin, and Wiechert, Wolfgang
- Subjects
PARETO analysis ,DECISION making ,EXPERIMENTAL design ,UNCERTAINTY ,MASS spectrometry ,MATHEMATICAL optimization - Abstract
Science revolves around the best way of conducting an experiment to obtain insightful results. Experiments with maximal information content can be found by computational experimental design (ED) strategies that identify optimal conditions under which to perform the experiment. Several criteria have been proposed to measure the information content, each emphasizing different aspects of the design goal, i.e., reduction of uncertainty. Where experiments are complex or expensive, second sight is at the budget governing the achievable amount of information. In this context, the design objectives cost and information gain are often incommensurable, though dependent. By casting the ED task into a multiple-criteria optimization problem, a set of trade-off designs is derived that approximates the Pareto-frontier which is instrumental for exploring preferable designs. In this work, we present a computational methodology for multiple-criteria ED of information-rich experiments that accounts for virtually any set of design criteria. The methodology is implemented for the case of
13 C metabolic flux analysis (MFA), which is arguably the most expensive type among the ‘omics’ technologies, featuring dozens of design parameters (tracer composition, analytical platform, measurement selection etc.). Supported by an innovative visualization scheme, we demonstrate with two realistic showcases that the use of multiple criteria reveals deep insights into the conflicting interplay between information carriers and cost factors that are not amendable to single-objective ED. For instance, tandem mass spectrometry turns out as best-in-class with respect to information gain, while it delivers this information quality cheaper than the other, routinely applied analytical technologies. Therewith, our Pareto approach to ED offers the investigator great flexibilities in the conception phase of a study to balance costs and benefits. [ABSTRACT FROM AUTHOR]- Published
- 2018
- Full Text
- View/download PDF
23. Wrangling distributed computing for high-throughput environmental science: An introduction to HTCondor.
- Author
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Erickson, Richard A., Fienen, Michael N., McCalla, S. Grace, Weiser, Emily L., Bower, Melvin L., Knudson, Jonathan M., and Thain, Greg
- Subjects
DISTRIBUTED computing ,BIOLOGISTS ,CLOUD computing ,OPEN source software ,COMPUTATIONAL biology - Abstract
Biologists and environmental scientists now routinely solve computational problems that were unimaginable a generation ago. Examples include processing geospatial data, analyzing -omics data, and running large-scale simulations. Conventional desktop computing cannot handle these tasks when they are large, and high-performance computing is not always available nor the most appropriate solution for all computationally intense problems. High-throughput computing (HTC) is one method for handling computationally intense research. In contrast to high-performance computing, which uses a single "supercomputer," HTC can distribute tasks over many computers (e.g., idle desktop computers, dedicated servers, or cloud-based resources). HTC facilities exist at many academic and government institutes and are relatively easy to create from commodity hardware. Additionally, consortia such as Open Science Grid facilitate HTC, and commercial entities sell cloud-based solutions for researchers who lack HTC at their institution. We provide an introduction to HTC for biologists and environmental scientists. Our examples from biology and the environmental sciences use HTCondor, an open source HTC system. [ABSTRACT FROM AUTHOR]
- Published
- 2018
- Full Text
- View/download PDF
24. Scabies in residential care homes: Modelling, inference and interventions for well-connected population sub-units.
- Author
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Kinyanjui, Timothy, Middleton, Jo, Güttel, Stefan, Cassell, Jackie, Ross, Joshua, and House, Thomas
- Subjects
SCABIES ,RESIDENTIAL care ,AGING ,INFECTIOUS disease transmission ,MARKOV chain Monte Carlo - Abstract
In the context of an ageing population, understanding the transmission of infectious diseases such as scabies through well-connected sub-units of the population, such as residential care homes, is particularly important for the design of efficient interventions to mitigate against the effects of those diseases. Here, we present a modelling methodology based on the efficient solution of a large-scale system of linear differential equations that allows statistical calibration of individual-based random models to real data on scabies in residential care homes. In particular, we review and benchmark different numerical methods for the integration of the differential equation system, and then select the most appropriate of these methods to perform inference using Markov chain Monte Carlo. We test the goodness-of-fit of this model using posterior predictive intervals and propagate forward the resulting parameter uncertainty in a Bayesian framework to consider the economic cost of delayed interventions against scabies, quantifying the benefits of prompt action in the event of detection. We also revisit the previous methodology used to assess the safety of treatments in small population sub-units—in this context ivermectin—and demonstrate that even a very slight relaxation of the implicit assumption of homogeneous death rates significantly increases the plausibility of the hypothesis that ivermectin does not cause excess mortality based upon the data of Barkwell and Shields [1]. [ABSTRACT FROM AUTHOR]
- Published
- 2018
- Full Text
- View/download PDF
25. Modeling the genetic relatedness of Plasmodium falciparum parasites following meiotic recombination and cotransmission.
- Author
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Wong, Wesley, Wenger, Edward A., Hartl, Daniel L., and Wirth, Dyann F.
- Subjects
PLASMODIUM falciparum genetics ,MALARIA transmission ,EPIDEMIOLOGICAL models ,MOSQUITO vectors ,POPULATION genetics - Abstract
Unlike in most pathogens, multiple-strain (polygenomic) infections of P. falciparum are frequently composed of genetic siblings. These genetic siblings are the result of sexual reproduction and can coinfect the same host when cotransmitted by the same mosquito. The degree with which coinfecting strains are related varies among infections and populations. Because sexual recombination occurs within the mosquito, the relatedness of cotransmitted strains could depend on transmission dynamics, but little is actually known of the factors that influence the relatedness of cotransmitted strains. Part of the uncertainty stems from an incomplete understanding of how within-host and within-vector dynamics affect cotransmission. Cotransmission is difficult to examine experimentally but can be explored using a computational model. We developed a malaria transmission model that simulates sexual reproduction in order to understand what determines the relatedness of cotransmitted strains. This study highlights how the relatedness of cotransmitted strains depends on both within-host and within-vector dynamics including the complexity of infection. We also used our transmission model to analyze the genetic relatedness of polygenomic infections following a series of multiple transmission events and examined the effects of superinfection. Understanding the factors that influence the relatedness of cotransmitted strains could lead to a better understanding of the population-genetic correlates of transmission and therefore be important for public health. [ABSTRACT FROM AUTHOR]
- Published
- 2018
- Full Text
- View/download PDF
26. MAGPIE: Simplifying access and execution of computational models in the life sciences.
- Author
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Baldow, Christoph, Salentin, Sebastian, Schroeder, Michael, Roeder, Ingo, and Glauche, Ingmar
- Subjects
LIFE sciences ,COMPUTER simulation ,SYSTEMS biology ,COMPUTATIONAL biology ,VIRTUAL machine systems - Abstract
Over the past decades, quantitative methods linking theory and observation became increasingly important in many areas of life science. Subsequently, a large number of mathematical and computational models has been developed. The BioModels database alone lists more than 140,000 Systems Biology Markup Language (SBML) models. However, while the exchange within specific models classes has been supported by standardisation and database efforts, the generic application and especially the re-use of models is still limited by practical issues such as easy and straight forward model execution. MAGPIE, a odeling and nalysis eneric latform with ntegrated valuation, closes this gap by providing a software platform for both, publishing and executing computational models without restrictions on the programming language, thereby combining a maximum on flexibility for programmers with easy handling for non-technical users. MAGPIE goes beyond classical SBML platforms by including all models, independent of the underlying programming language, ranging from simple script models to complex data integration and computations. We demonstrate the versatility of MAGPIE using four prototypic example cases. We also outline the potential of MAGPIE to improve transparency and reproducibility of computational models in life sciences. A demo server is available at magpie.imb.medizin.tu-dresden.de. [ABSTRACT FROM AUTHOR]
- Published
- 2017
- Full Text
- View/download PDF
27. Ten simple rules for writing a career development award proposal.
- Author
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Botham, Crystal M., Arribere, Joshua A., Brubaker, Sky W., and Beier, Kevin T.
- Subjects
GRANT writing ,CAREER development ,GRANTS (Money) ,AUTHORSHIP ,MENTORING in the professions ,MENTORING - Abstract
The article presents rules for writing a proposal for a career development grant. Applicants are advised to have three months of full-time effort for completing the application, to use the review criteria as a guide for writing a proposal and to write a clear and concise proposal. The importance of having a mentoring team during the proposed funding program is discussed.
- Published
- 2017
- Full Text
- View/download PDF
28. fluEvidenceSynthesis: An R package for evidence synthesis based analysis of epidemiological outbreaks.
- Author
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van Leeuwen, Edwin, Klepac, Petra, Thorrington, Dominic, Pebody, Richard, and Baguelin, Marc
- Subjects
EPIDEMIOLOGICAL models ,DISEASE outbreaks ,PUBLIC health ,INFLUENZA vaccines ,BAYESIAN analysis - Abstract
Public health related decisions often have to balance the cost of intervention strategies with the benefit of the reduction in disease burden. While the cost can often be inferred, forward modelling of the effect of different intervention options is complicated and disease specific. Here we introduce a package that is aimed to simplify this process. The package allows one to infer parameters using a Bayesian approach, perform forward modelling of the likely results of the proposed intervention and finally perform cost effectiveness analysis of the results. The package is based on a method previously used in the UK to inform vaccination strategies for influenza, with extensions to make it easily adaptable to other diseases and data sources. [ABSTRACT FROM AUTHOR]
- Published
- 2017
- Full Text
- View/download PDF
29. Ten simple rules in considering a career in academia versus government.
- Author
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Bourne, Philip E.
- Subjects
ACADEMIC employment ,CIVIL service positions ,VOCATIONAL guidance ,VOCATIONAL interests ,DECISION making - Abstract
The author reflects on rules to be followed while making a career decision, which includes selection of career between academic research based career and the non-research government career. He states that both the work environments have a very large scope if chosen as career. The similarities and differences between the two fields is presented from the author's point of view.
- Published
- 2017
- Full Text
- View/download PDF
30. C-reactive protein upregulates the whole blood expression of CD59 - an integrative analysis.
- Author
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Lepik, Kaido, Annilo, Tarmo, Kukuškina, Viktorija, Kisand, Kai, Kutalik, Zoltán, Peterson, Pärt, Peterson, Hedi, and null, null
- Subjects
C-reactive protein ,BACTERIAL diseases ,VIRUS diseases ,GENE expression ,INFLAMMATION ,CHRONIC diseases - Abstract
Elevated C-reactive protein (CRP) concentrations in the blood are associated with acute and chronic infections and inflammation. Nevertheless, the functional role of increased CRP in multiple bacterial and viral infections as well as in chronic inflammatory diseases remains unclear. Here, we studied the relationship between CRP and gene expression levels in the blood in 491 individuals from the Estonian Biobank cohort, to elucidate the role of CRP in these inflammatory mechanisms. As a result, we identified a set of 1,614 genes associated with changes in CRP levels with a high proportion of interferon-stimulated genes. Further, we performed likelihood-based causality model selection and Mendelian randomization analysis to discover causal links between CRP and the expression of CRP-associated genes. Strikingly, our computational analysis and cell culture stimulation assays revealed increased CRP levels to drive the expression of complement regulatory protein CD59, suggesting CRP to have a critical role in protecting blood cells from the adverse effects of the immune defence system. Our results show the benefit of integrative analysis approaches in hypothesis-free uncovering of causal relationships between traits. [ABSTRACT FROM AUTHOR]
- Published
- 2017
- Full Text
- View/download PDF
31. Ten Simple Rules for a Bioinformatics Journal Club
- Author
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Michael L. Walker, Timothy Rice, Harriet Dashnow, Jocelyn Sietsma Penington, and Andrew Lonsdale
- Subjects
0301 basic medicine ,Time Factors ,Economics ,Computer science ,Social Sciences ,Biologists ,Scientific literature ,Bioinformatics ,Coffee ,Attitudes (Psychology) ,Social group ,Database and Informatics Methods ,Learning and Memory ,Sociology ,Psychology ,lcsh:QH301-705.5 ,Careers ,Ecology ,Attendance ,Social Communication ,Professions ,Editorial ,Computational Theory and Mathematics ,Modeling and Simulation ,Analytical skill ,Club ,Periodicals as Topic ,Journal club ,Employment ,Research and Analysis Methods ,Peer Group ,Critical mass (sociodynamics) ,Human Learning ,03 medical and health sciences ,Cellular and Molecular Neuroscience ,Genetics ,Learning ,Humans ,Molecular Biology ,Ecology, Evolution, Behavior and Systematics ,Cognitive Psychology ,Biology and Life Sciences ,Relaxation (Psychology) ,Computational Biology ,Peer group ,Communications ,030104 developmental biology ,lcsh:Biology (General) ,Labor Economics ,People and Places ,Cognitive Science ,Scientists ,Population Groupings ,Neuroscience - Abstract
As science becomes increasingly interdisciplinary, we are expected to acquire both breadth of knowledge and depth of expertise. In bioinformatics, this is especially true. Keeping up to date with major techniques across multiple specialisations can be daunting, but you need not face it alone. A journal club is an excellent way to take in the scientific literature, keep up with developments in your field, and hone your communication and analytical skills. In general, a journal club is a group of people who meet regularly to discuss one or more scientific papers. The structure of such a club can vary. In the more traditional format, an individual studies a paper and then presents it to the group, usually in the form of PowerPoint slides, with time for questions. In some institutions, the journal club is for students only, designed to fulfill the requirements of a course or postgraduate program; attendance is obligatory, the scope of the literature is narrow, and the format is prescribed. The preparation of slides and a lecture may be required. Other kinds of journal clubs are just lab meetings in disguise, with the usual lab head and group members in attendance and one member nominated to present the paper. A formal style often fits well within an established academic structure—but what if your discipline is emerging? Consider the field of bioinformatics. Expertise may be spread across departments and institutions, and there may not be an obvious place or critical mass in any one lab for a traditional journal club. Research students, “pet bioinformaticians,” [1] and those interested in bioinformatics from adjoining fields all need a place to gather. We are pleased to offer an alternative structure to address this situation—an informal journal club, designed to bring together a diversity of backgrounds and career stages to discuss bioinformatics while building a network of like-minded peers. Additional benefits of such a journal club may include friendship and breakfast (see Rule 2)! We thoroughly recommend it to anyone who asks (as well as those who don’t). While this advice is drawn from our experiences in the Parkville Bioinformatics Journal Club, it is applicable to developing informal journal clubs of all disciplines. The advice contained in these rules will also help those who want to spice up their existing formal format. So don’t be a “lonely bioinformatician”[1], create a journal club! Follow these Ten Simple Rules to find out how.
- Published
- 2016
32. Epidemiological and economic impact of pandemic influenza in Chicago: Priorities for vaccine interventions.
- Author
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Dorratoltaj, Nargesalsadat, Marathe, Achla, Lewis, Bryan L., Swarup, Samarth, Eubank, Stephen G., and Abbas, Kaja M.
- Subjects
INFLUENZA treatment ,H1N1 influenza ,VACCINES ,PANDEMICS ,EPIDEMIOLOGY ,PUBLIC health - Abstract
The study objective is to estimate the epidemiological and economic impact of vaccine interventions during influenza pandemics in Chicago, and assist in vaccine intervention priorities. Scenarios of delay in vaccine introduction with limited vaccine efficacy and limited supplies are not unlikely in future influenza pandemics, as in the 2009 H1N1 influenza pandemic. We simulated influenza pandemics in Chicago using agent-based transmission dynamic modeling. Population was distributed among high-risk and non-high risk among 0–19, 20–64 and 65+ years subpopulations. Different attack rate scenarios for catastrophic (30.15%), strong (21.96%), and moderate (11.73%) influenza pandemics were compared against vaccine intervention scenarios, at 40% coverage, 40% efficacy, and unit cost of $28.62. Sensitivity analysis for vaccine compliance, vaccine efficacy and vaccine start date was also conducted. Vaccine prioritization criteria include risk of death, total deaths, net benefits, and return on investment. The risk of death is the highest among the high-risk 65+ years subpopulation in the catastrophic influenza pandemic, and highest among the high-risk 0–19 years subpopulation in the strong and moderate influenza pandemics. The proportion of total deaths and net benefits are the highest among the high-risk 20–64 years subpopulation in the catastrophic, strong and moderate influenza pandemics. The return on investment is the highest in the high-risk 0–19 years subpopulation in the catastrophic, strong and moderate influenza pandemics. Based on risk of death and return on investment, high-risk groups of the three age group subpopulations can be prioritized for vaccination, and the vaccine interventions are cost saving for all age and risk groups. The attack rates among the children are higher than among the adults and seniors in the catastrophic, strong, and moderate influenza pandemic scenarios, due to their larger social contact network and homophilous interactions in school. Based on return on investment and higher attack rates among children, we recommend prioritizing children (0–19 years) and seniors (65+ years) after high-risk groups for influenza vaccination during times of limited vaccine supplies. Based on risk of death, we recommend prioritizing seniors (65+ years) after high-risk groups for influenza vaccination during times of limited vaccine supplies. [ABSTRACT FROM AUTHOR]
- Published
- 2017
- Full Text
- View/download PDF
33. Ten simple rules for surviving an interdisciplinary PhD.
- Author
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Demharter, Samuel, Pearce, Nicholas, Beattie, Kylie, Frost, Isabel, Leem, Jinwoo, Martin, Alistair, Oppenheimer, Robert, Regep, Cristian, Rukat, Tammo, Skates, Alexander, Trendel, Nicola, Gavaghan, David J., Deane, Charlotte M., and Knapp, Bernhard
- Subjects
INTERDISCIPLINARY approach to knowledge ,DOCTOR of philosophy degree ,INTERDISCIPLINARY education ,INTELLECTUAL freedom ,PLANNING ,CAREER development - Abstract
The article focuses on ten rules for surviving and thriving in an interdisciplinary doctor of philosophy (PhD) setting, highlighting the importance of having a comprehensive plan and intellectual freedom, among others. Topics discussed include organizing regular meetings with supervisors and collaborators for collective planning, fostering relationships with researchers from diverse backgrounds, and building required competencies and skills to pursue one's career.
- Published
- 2017
- Full Text
- View/download PDF
34. Ten simple rules to make the most out of your undergraduate research career.
- Author
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Yu, Megan and Kuo, Yu-Min
- Subjects
RESEARCH ,UNDERGRADUATES ,CAREER development ,MASSIVE open online courses ,RESEARCH personnel - Abstract
The article discusses several rules for undergraduates to help them intellectually enrich their research experiences, in view of benefits of research in undergraduate education, and their struggle in understanding purpose of work. Topics include need for undergraduates to start early to explore research interests and goals for career; having a background knowledge in the research area using resources like Massive Open Online Courses; and having positive relationships with research colleagues.
- Published
- 2017
- Full Text
- View/download PDF
35. Quantifying the Value of Perfect Information in Emergency Vaccination Campaigns.
- Author
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Bradbury, Naomi V., Probert, William J. M., Shea, Katriona, Runge, Michael C., Fonnesbeck, Christopher J., Keeling, Matt J., Ferrari, Matthew J., and Tildesley, Michael J.
- Subjects
FOOT & mouth disease vaccines ,ECONOMICS ,LIVESTOCK diseases ,VACCINE effectiveness ,IMMUNE response ,VACCINATION ,THERAPEUTICS - Abstract
Foot-and-mouth disease outbreaks in non-endemic countries can lead to large economic costs and livestock losses but the use of vaccination has been contentious, partly due to uncertainty about emergency FMD vaccination. Value of information methods can be applied to disease outbreak problems such as FMD in order to investigate the performance improvement from resolving uncertainties. Here we calculate the expected value of resolving uncertainty about vaccine efficacy, time delay to immunity after vaccination and daily vaccination capacity for a hypothetical FMD outbreak in the UK. If it were possible to resolve all uncertainty prior to the introduction of control, we could expect savings of £55 million in outbreak cost, 221,900 livestock culled and 4.3 days of outbreak duration. All vaccination strategies were found to be preferable to a culling only strategy. However, the optimal vaccination radius was found to be highly dependent upon vaccination capacity for all management objectives. We calculate that by resolving the uncertainty surrounding vaccination capacity we would expect to return over 85% of the above savings, regardless of management objective. It may be possible to resolve uncertainty about daily vaccination capacity before an outbreak, and this would enable decision makers to select the optimal control action via careful contingency planning. [ABSTRACT FROM AUTHOR]
- Published
- 2017
- Full Text
- View/download PDF
36. Ten Simple Rules for Developing a Successful Research Proposal in Brazil.
- Author
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de Oliveira, Dyoni M., Buckeridge, Marcos S., and dos Santos, Wanderley D.
- Subjects
RESEARCH grants ,FEDERAL aid to research ,ACADEMIC degrees ,DOCTORAL degree ,SCHOLARSHIPS - Abstract
The article describes the ten rules for the development of a successful research grant proposal and MSc and PhD degree fellowships. Topics include defining the problem clearly, formulating falsifiable hypotheses and including preliminary data, and establishing clear objectives. Also suggested is carefully estimating the duration and requirements of experimental procedures.
- Published
- 2017
- Full Text
- View/download PDF
37. THE REAL McCOIL: A method for the concurrent estimation of the complexity of infection and SNP allele frequency for malaria parasites.
- Author
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Chang, Hsiao-Han, Worby, Colin J., Yeka, Adoke, Nankabirwa, Joaniter, Kamya, Moses R., Staedke, Sarah G., Dorsey, Grant, Murphy, Maxwell, Neafsey, Daniel E., Jeffreys, Anna E., Hubbart, Christina, Rockett, Kirk A., Amato, Roberto, Kwiatkowski, Dominic P., Buckee, Caroline, and Greenhouse, Bryan
- Subjects
BIOINFORMATICS software ,MALARIA transmission ,SINGLE nucleotide polymorphisms - Abstract
As many malaria-endemic countries move towards elimination of Plasmodium falciparum, the most virulent human malaria parasite, effective tools for monitoring malaria epidemiology are urgent priorities. P. falciparum population genetic approaches offer promising tools for understanding transmission and spread of the disease, but a high prevalence of multi-clone or polygenomic infections can render estimation of even the most basic parameters, such as allele frequencies, challenging. A previous method, COIL, was developed to estimate complexity of infection (COI) from single nucleotide polymorphism (SNP) data, but relies on monogenomic infections to estimate allele frequencies or requires external allele frequency data which may not available. Estimates limited to monogenomic infections may not be representative, however, and when the average COI is high, they can be difficult or impossible to obtain. Therefore, we developed THE REAL McCOIL, Turning HEterozygous SNP data into Robust Estimates of ALelle frequency, via Markov chain Monte Carlo, and Complexity Of Infection using Likelihood, to incorporate polygenomic samples and simultaneously estimate allele frequency and COI. This approach was tested via simulations then applied to SNP data from cross-sectional surveys performed in three Ugandan sites with varying malaria transmission. We show that THE REAL McCOIL consistently outperforms COIL on simulated data, particularly when most infections are polygenomic. Using field data we show that, unlike with COIL, we can distinguish epidemiologically relevant differences in COI between and within these sites. Surprisingly, for example, we estimated high average COI in a peri-urban subregion with lower transmission intensity, suggesting that many of these cases were imported from surrounding regions with higher transmission intensity. THE REAL McCOIL therefore provides a robust tool for understanding the molecular epidemiology of malaria across transmission settings. [ABSTRACT FROM AUTHOR]
- Published
- 2017
- Full Text
- View/download PDF
38. Novel Covariance-Based Neutrality Test of Time-Series Data Reveals Asymmetries in Ecological and Economic Systems.
- Author
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Washburne, Alex D., Burby, Joshua W., and Lacker, Daniel
- Subjects
TIME series analysis ,SYMMETRY (Biology) ,ANALYSIS of covariance ,ECOSYSTEMS ,ECONOMIC systems ,COMPETITION (Biology) ,POPULATION genetics - Abstract
Systems as diverse as the interacting species in a community, alleles at a genetic locus, and companies in a market are characterized by competition (over resources, space, capital, etc) and adaptation. Neutral theory, built around the hypothesis that individual performance is independent of group membership, has found utility across the disciplines of ecology, population genetics, and economics, both because of the success of the neutral hypothesis in predicting system properties and because deviations from these predictions provide information about the underlying dynamics. However, most tests of neutrality are weak, based on static system properties such as species-abundance distributions or the number of singletons in a sample. Time-series data provide a window onto a system’s dynamics, and should furnish tests of the neutral hypothesis that are more powerful to detect deviations from neutrality and more informative about to the type of competitive asymmetry that drives the deviation. Here, we present a neutrality test for time-series data. We apply this test to several microbial time-series and financial time-series and find that most of these systems are not neutral. Our test isolates the covariance structure of neutral competition, thus facilitating further exploration of the nature of asymmetry in the covariance structure of competitive systems. Much like neutrality tests from population genetics that use relative abundance distributions have enabled researchers to scan entire genomes for genes under selection, we anticipate our time-series test will be useful for quick significance tests of neutrality across a range of ecological, economic, and sociological systems for which time-series data are available. Future work can use our test to categorize and compare the dynamic fingerprints of particular competitive asymmetries (frequency dependence, volatility smiles, etc) to improve forecasting and management of complex adaptive systems. [ABSTRACT FROM AUTHOR]
- Published
- 2016
- Full Text
- View/download PDF
39. Ten simple rules for organizing a bioinformatics training course in low- and middle-income countries
- Author
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Patricia Carvajal-López, Piraveen Gopalasingam, Amel Ghouila, Sarah L. Morgan, Guilherme Oliveira, Verena Ras, Paballo Abel Chauke, Alice Matimba, Alejandro Reyes, Selene L. Fernandez-Valverde, Nicola Mulder, Marco Cristancho, Javier De Las Rivas, Fatma Z. Guerfali, Victoria Dominguez Del Angel, Benjamin Moore, Wellcome Trust, National Institutes of Health (US), Biotechnology and Biological Sciences Research Council (UK), Global Challenges Research Fund, Instituto de Salud Carlos III, Consejo Superior de Investigaciones Científicas (España), Universidad de Salamanca, and Instituto Nacional de Bioinformática (España)
- Subjects
Budgets ,Financial Management ,Economics ,Computer science ,Social Sciences ,Economic Geography ,Database and Informatics Methods ,Learning and Memory ,0302 clinical medicine ,Sociology ,Simple (abstract algebra) ,Psychology ,Biology (General) ,0303 health sciences ,Geography ,Ecology ,4. Education ,Software Engineering ,ComputingMilieux_GENERAL ,Professions ,Interdisciplinary Placement ,Editorial ,Computational Theory and Mathematics ,Modeling and Simulation ,Low and Middle Income Countries ,Educational Status ,Engineering and Technology ,Workshops ,Curriculum ,Human learning ,Computer and Information Sciences ,Coronavirus disease 2019 (COVID-19) ,Bioinformatics ,QH301-705.5 ,Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) ,Training course ,MEDLINE ,Research and Analysis Methods ,Education ,Computer Software ,Human Learning ,03 medical and health sciences ,Cellular and Molecular Neuroscience ,Genetics ,Learning ,Animals ,Humans ,Molecular Biology ,Developing Countries ,Ecology, Evolution, Behavior and Systematics ,030304 developmental biology ,Cognitive Psychology ,Sustainability science ,Biology and Life Sciences ,Computational Biology ,Data science ,Trainees ,Low and middle income countries ,Instructors ,People and Places ,Earth Sciences ,Cognitive Science ,Population Groupings ,Finance ,030217 neurology & neurosurgery ,Neuroscience - Abstract
© 2021 Moore et al., Bioinformatics training is required at every stage of a scientist’s research career. Continual bioinformatics training allows exposure to an ever-changing and growing repertoire of techniques and databases, and so biologists, computational scientists, and healthcare practitioners are all seeking learning opportunities in the use of computational resources and tools designed for data storage, retrieval, and analysis. There are abundant opportunities for accessing bioinformatics training for scientists in high-income countries (HICs), with well-equipped facilities and participants and trainers requiring minimal travel and financial costs alongside a range of general advice for developing short bioinformatics training courses [1–3]. However, regionally targeted bioinformatics training in low- and middle-income countries (LMICs) often requires more extensive local and external support, organization, and travel. Due to the limited expertise in bioinformatics in LMICs in general, most bioinformatics training requires a fair amount of collaboration with experts beyond the local community, country, or region. A common model of training, used as the basis of this article, includes a local host collaborating with local, regional, and international experts gathering to train local or regional participants. Recently, there has been a growth of capacity strengthening initiatives in LMICs, such as the Pan African Bioinformatics Network for Human Heredity and Health in Africa (H3ABioNet) Initiative [4–6], the Capacity Building for Bioinformatics in Latin America (CABANA) Project [7], the Asia Pacific BioInformatics Network (APBioNet) [8], and the Wellcome Connecting Science Courses and Conferences program [9]. One of the important strands of these initiatives is a drive to organize and deliver valuable bioinformatics training, but organizing and delivering short bioinformatics training workshops in an LMIC present a unique set of challenges. This paper attempts to build upon the sage advice for organizing bioinformatics workshops with specific guidance for organizing and delivering them in LMICs. It describes the processes to follow in organizing courses taking into consideration the low-resource setting. We should also note that LMICs are not a monolithic group and that setting, context, temporality, and specific location matters. LMICs are a complex regional grouping [10] and should be treated as such; however, we will present some common lessons that we hope will help organizers and trainers of bioinformatics training events in LMICs to navigate the often different, challenging, and rewarding experience., The authors who contributed to this manuscript are funded as follows: BM receives salary support from Wellcome Trust grants [WT108749/Z/15/Z, WT108749/Z/15/A], PC, VR, NM, AG’s salaries are funded in whole, or in part, by the NIH Common Fund H3ABioNet grant [U24HG006941], MC, SLFV, AR, PG, PCL’s salaries were partly funded by the UKRI-BBSRC ‘Capacity building for bioinformatics in Latin America’ (CABANA) grant, on behalf of the Global Challenges Research Fund [BB/P027849/1], JDLR is funded by ISCiii AES [ref. PI18/00591] at the CSIC/USAL (Spain) and by CYTED, RIABIO (Red Iberoamericana 521RT0118), AM’s salary is funded by [WT206194/Z/17/Z], GO is funded by the CABANA grant and SM is funded by the EMBL-EBI.
- Published
- 2021
40. Ten Simple Rules for Curating and Facilitating Small Workshops.
- Author
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McInerny, Greg J.
- Subjects
FORUMS ,WORKSHOPS (Facilities) -- Design & construction ,RESEARCH ,TOPIC & comment (Grammar) ,DISCUSSION ,TIME perspective ,INTERACTION model (Communication) - Abstract
The article discusses the creation of good workshops which could be in a diverse form and fit different goals. This is needed for exploring a single research topic, initiation of working group, and interdisciplinary collaborations. It requires attendees, timetables, and interactions. Topics discussed processes in facilitating workshops including assessment on past success and failures, developing of workshop name, and preparing for speakers speech.
- Published
- 2016
- Full Text
- View/download PDF
41. Intrinsic Valuation of Information in Decision Making under Uncertainty.
- Author
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Bennett, Daniel, Bode, Stefan, Brydevall, Maja, Warren, Hayley, and Murawski, Carsten
- Subjects
DECISION making ,VALUATION policy ,DEBT-to-equity ratio ,RATIO analysis ,FINANCIAL ratios - Abstract
In a dynamic world, an accurate model of the environment is vital for survival, and agents ought regularly to seek out new information with which to update their world models. This aspect of behaviour is not captured well by classical theories of decision making, and the cognitive mechanisms of information seeking are poorly understood. In particular, it is not known whether information is valued only for its instrumental use, or whether humans also assign it a non-instrumental intrinsic value. To address this question, the present study assessed preference for non-instrumental information among 80 healthy participants in two experiments. Participants performed a novel information preference task in which they could choose to pay a monetary cost to receive advance information about the outcome of a monetary lottery. Importantly, acquiring information did not alter lottery outcome probabilities. We found that participants were willing to incur considerable monetary costs to acquire payoff-irrelevant information about the lottery outcome. This behaviour was well explained by a computational cognitive model in which information preference resulted from aversion to temporally prolonged uncertainty. These results strongly suggest that humans assign an intrinsic value to information in a manner inconsistent with normative accounts of decision making under uncertainty. This intrinsic value may be associated with adaptive behaviour in real-world environments by producing a bias towards exploratory and information-seeking behaviour. [ABSTRACT FROM AUTHOR]
- Published
- 2016
- Full Text
- View/download PDF
42. Continuing Education Workshops in Bioinformatics Positively Impact Research and Careers.
- Author
-
Brazas, Michelle D. and Ouellette, B. F. Francis
- Subjects
BIOINFORMATICS ,INFORMATION science ,COMPUTERS in biology ,CONTINUING education ,ADULT education workshops - Abstract
Bioinformatics.ca has been hosting continuing education programs in introductory and advanced bioinformatics topics in Canada since 1999 and has trained more than 2,000 participants to date. These workshops have been adapted over the years to keep pace with advances in both science and technology as well as the changing landscape in available learning modalities and the bioinformatics training needs of our audience. Post-workshop surveys have been a mandatory component of each workshop and are used to ensure appropriate adjustments are made to workshops to maximize learning. However, neither bioinformatics.ca nor others offering similar training programs have explored the long-term impact of bioinformatics continuing education training. Bioinformatics.ca recently initiated a look back on the impact its workshops have had on the career trajectories, research outcomes, publications, and collaborations of its participants. Using an anonymous online survey, bioinformatics.ca analyzed responses from those surveyed and discovered its workshops have had a positive impact on collaborations, research, publications, and career progression. [ABSTRACT FROM AUTHOR]
- Published
- 2016
- Full Text
- View/download PDF
43. Principles for data analysis workflows
- Author
-
Váleri N. Vásquez, Ciera C. Martinez, and Sara Stoudt
- Subjects
FOS: Computer and information sciences ,Data Analysis ,0301 basic medicine ,Science and Technology Workforce ,Economics ,Computer science ,Social Sciences ,Design elements and principles ,Careers in Research ,Workflow ,Computer Science - Computers and Society ,0302 clinical medicine ,Biology (General) ,Data Management ,Careers ,Ecology ,Software Development ,Software Engineering ,Research Assessment ,Reproducibility ,Professions ,Computational Theory and Mathematics ,Modeling and Simulation ,Engineering and Technology ,Raw data ,Employment ,Computer and Information Sciences ,Science Policy ,Process (engineering) ,QH301-705.5 ,Research and Analysis Methods ,Phase (combat) ,Education ,Computer Software ,03 medical and health sciences ,Cellular and Molecular Neuroscience ,Computers and Society (cs.CY) ,Genetics ,Humans ,Molecular Biology ,Ecology, Evolution, Behavior and Systematics ,Software Tools ,business.industry ,Data Science ,Software development ,Computational Biology ,Data science ,030104 developmental biology ,Labor Economics ,People and Places ,Scientists ,Population Groupings ,business ,Software ,030217 neurology & neurosurgery - Abstract
A systematic and reproducible “workflow”—the process that moves a scientific investigation from raw data to coherent research question to insightful contribution—should be a fundamental part of academic data-intensive research practice. In this paper, we elaborate basic principles of a reproducible data analysis workflow by defining 3 phases: the Explore, Refine, and Produce Phases. Each phase is roughly centered around the audience to whom research decisions, methodologies, and results are being immediately communicated. Importantly, each phase can also give rise to a number of research products beyond traditional academic publications. Where relevant, we draw analogies between design principles and established practice in software development. The guidance provided here is not intended to be a strict rulebook; rather, the suggestions for practices and tools to advance reproducible, sound data-intensive analysis may furnish support for both students new to research and current researchers who are new to data-intensive work.
- Published
- 2021
44. Anticipation and Choice Heuristics in the Dynamic Consumption of Pain Relief.
- Author
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Story, Giles W., Vlaev, Ivo, Dayan, Peter, Seymour, Ben, Darzi, Ara, and Dolan, Raymond J.
- Subjects
HEURISTIC ,ANALGESIA ,EXPECTATION (Philosophy) ,ECONOMICS ,AVERSIVE stimuli - Abstract
Humans frequently need to allocate resources across multiple time-steps. Economic theory proposes that subjects do so according to a stable set of intertemporal preferences, but the computational demands of such decisions encourage the use of formally less competent heuristics. Few empirical studies have examined dynamic resource allocation decisions systematically. Here we conducted an experiment involving the dynamic consumption over approximately 15 minutes of a limited budget of relief from moderately painful stimuli. We had previously elicited the participants’ time preferences for the same painful stimuli in one-off choices, allowing us to assess self-consistency. Participants exhibited three characteristic behaviors: saving relief until the end, spreading relief across time, and early spending, of which the last was markedly less prominent. The likelihood that behavior was heuristic rather than normative is suggested by the weak correspondence between one-off and dynamic choices. We show that the consumption choices are consistent with a combination of simple heuristics involving early-spending, spreading or saving of relief until the end, with subjects predominantly exhibiting the last two. [ABSTRACT FROM AUTHOR]
- Published
- 2015
- Full Text
- View/download PDF
45. Some Work and Some Play: Microscopic and Macroscopic Approaches to Labor and Leisure.
- Author
-
Niyogi, Ritwik K., Shizgal, Peter, and Dayan, Peter
- Subjects
WORK & leisure ,COMPUTATIONAL biology ,ECOLOGICAL economics ,REWARD (Psychology) ,NEUROSCIENCES ,MARKOV processes - Abstract
Given the option, humans and other animals elect to distribute their time between work and leisure, rather than choosing all of one and none of the other. Traditional accounts of partial allocation have characterised behavior on a macroscopic timescale, reporting and studying the mean times spent in work or leisure. However, averaging over the more microscopic processes that govern choices is known to pose tricky theoretical problems, and also eschews any possibility of direct contact with the neural computations involved. We develop a microscopic framework, formalized as a semi-Markov decision process with possibly stochastic choices, in which subjects approximately maximise their expected returns by making momentary commitments to one or other activity. We show macroscopic utilities that arise from microscopic ones, and demonstrate how facets such as imperfect substitutability can arise in a more straightforward microscopic manner. [ABSTRACT FROM AUTHOR]
- Published
- 2014
- Full Text
- View/download PDF
46. De Novo Design and Experimental Characterization of Ultrashort Self-Associating Peptides.
- Author
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Smadbeck, James, Chan, Kiat Hwa, Khoury, George A., Xue, Bo, Robinson, Robert C., Hauser, Charlotte A. E., and Floudas, Christodoulos A.
- Subjects
PEPTIDES ,EXPERIMENTAL biology ,CYTOSKELETON ,COMPUTATIONAL biology ,MATHEMATICAL sequences - Abstract
Self-association is a common phenomenon in biology and one that can have positive and negative impacts, from the construction of the architectural cytoskeleton of cells to the formation of fibrils in amyloid diseases. Understanding the nature and mechanisms of self-association is important for modulating these systems and in creating biologically-inspired materials. Here, we present a two-stage de novo peptide design framework that can generate novel self-associating peptide systems. The first stage uses a simulated multimeric template structure as input into the optimization-based Sequence Selection to generate low potential energy sequences. The second stage is a computational validation procedure that calculates Fold Specificity and/or Approximate Association Affinity (K
* association ) based on metrics that we have devised for multimeric systems. This framework was applied to the design of self-associating tripeptides using the known self-associating tripeptide, Ac-IVD, as a structural template. Six computationally predicted tripeptides (Ac-LVE, Ac-YYD, Ac-LLE, Ac-YLD, Ac-MYD, Ac-VIE) were chosen for experimental validation in order to illustrate the self-association outcomes predicted by the three metrics. Self-association and electron microscopy studies revealed that Ac-LLE formed bead-like microstructures, Ac-LVE and Ac-YYD formed fibrillar aggregates, Ac-VIE and Ac-MYD formed hydrogels, and Ac-YLD crystallized under ambient conditions. An X-ray crystallographic study was carried out on a single crystal of Ac-YLD, which revealed that each molecule adopts a β-strand conformation that stack together to form parallel β-sheets. As an additional validation of the approach, the hydrogel-forming sequences of Ac-MYD and Ac-VIE were shuffled. The shuffled sequences were computationally predicted to have lower K* association values and were experimentally verified to not form hydrogels. This illustrates the robustness of the framework in predicting self-associating tripeptides. We expect that this enhanced multimeric de novo peptide design framework will find future application in creating novel self-associating peptides based on unnatural amino acids, and inhibitor peptides of detrimental self-aggregating biological proteins. [ABSTRACT FROM AUTHOR]- Published
- 2014
- Full Text
- View/download PDF
47. Optimal Screening Strategies for Healthcare Associated Infections in a Multi-Institutional Setting.
- Author
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Miller, Aaron C., Polgreen, Linnea A., and Polgreen, Philip M.
- Subjects
HEALTH facility safety measures ,MEDICAL screening ,DISEASE prevalence ,DIAGNOSIS ,PATIENT safety ,DECISION making ,EPIDEMIOLOGICAL models ,EPIDEMIOLOGY ,MEDICAL economics - Abstract
Health institutions may choose to screen newly admitted patients for the presence of disease in order to reduce disease prevalence within the institution. Screening is costly, and institutions must judiciously choose which patients they wish to screen based on the dynamics of disease transmission. Since potentially infected patients move between different health institutions, the screening and treatment decisions of one institution will affect the optimal decisions of others; an institution might choose to “free-ride” off the screening and treatment decisions of neighboring institutions. We develop a theoretical model of the strategic decision problem facing a health care institution choosing to screen newly admitted patients. The model incorporates an SIS compartmental model of disease transmission into a game theoretic model of strategic decision-making. Using this setup, we are able to analyze how optimal screening is influenced by disease parameters, such as the efficacy of treatment, the disease recovery rate and the movement of patients. We find that the optimal screening level is lower for diseases that have more effective treatments. Our model also allows us to analyze how the optimal screening level varies with the number of decision makers involved in the screening process. We show that when institutions are more autonomous in selecting whom to screen, they will choose to screen at a lower rate than when screening decisions are more centralized. Results also suggest that centralized screening decisions have a greater impact on disease prevalence when the availability or efficacy of treatment is low. Our model provides insight into the factors one should consider when choosing whether to set a mandated screening policy. We find that screening mandates set at a centralized level (i.e. state or national) will have a greater impact on the control of infectious disease. [ABSTRACT FROM AUTHOR]
- Published
- 2014
- Full Text
- View/download PDF
48. Optima TB: A tool to help optimally allocate tuberculosis spending
- Author
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Henadz Hurevich, Jolene Skordis, David Wilson, Lara Goscé, Anna Roberts, Jasmina Panovska-Griffiths, Azfar Hussain, Sherrie L Kelly, Nicole Fraser-Hurt, Robyn M. Stuart, Tom Palmer, Marelize Gorgens, Hassan Haghparast-Bidgoli, Romesh G. Abeysuriya, Gerard Joseph Abou Jaoude, Rowan Martin-Hughes, Ibrahim Abubakar, Cliff C. Kerr, Sarah Jarvis, David J. Kedziora, Clemens Benedikt, Dzmitry Klimuk, Feng Zhao, Nejma Cheikh, and Alena Skrahina
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Bacterial Diseases ,Male ,Republic of Belarus ,Epidemiology ,Economics ,Service delivery framework ,Extensively Drug-Resistant Tuberculosis ,Cost-Benefit Analysis ,Psychological intervention ,Social Sciences ,Geographical Locations ,Medical Conditions ,Medicine and Health Sciences ,Prevalence ,Prospective Studies ,Biology (General) ,Child ,Aged, 80 and over ,education.field_of_study ,Ecology ,Pharmaceutics ,Multi-Drug-Resistant Tuberculosis ,Belarus ,Health Care Costs ,Middle Aged ,Europe ,Infectious Diseases ,Models, Economic ,Computational Theory and Mathematics ,Child, Preschool ,Modeling and Simulation ,General partnership ,Physical Sciences ,Female ,01 Mathematical Sciences, 06 Biological Sciences, 08 Information and Computing Sciences ,Algorithms ,Research Article ,Optimization ,Adult ,medicine.medical_specialty ,Tuberculosis ,Adolescent ,QH301-705.5 ,Bioinformatics ,Population ,Models, Biological ,Resource Allocation ,Young Adult ,Cellular and Molecular Neuroscience ,Drug Therapy ,Environmental health ,Genetics ,medicine ,Income country ,Humans ,education ,Molecular Biology ,Ecology, Evolution, Behavior and Systematics ,Mass screening ,Aged ,Infant, Newborn ,Computational Biology ,Infant ,Tropical Diseases ,medicine.disease ,People and Places ,Business ,Mathematics ,Finance ,Software - Abstract
Approximately 85% of tuberculosis (TB) related deaths occur in low- and middle-income countries where health resources are scarce. Effective priority setting is required to maximise the impact of limited budgets. The Optima TB tool has been developed to support analytical capacity and inform evidence-based priority setting processes for TB health benefits package design. This paper outlines the Optima TB framework and how it was applied in Belarus, an upper-middle income country in Eastern Europe with a relatively high burden of TB. Optima TB is a population-based disease transmission model, with programmatic cost functions and an optimisation algorithm. Modelled populations include age-differentiated general populations and higher-risk populations such as people living with HIV. Populations and prospective interventions are defined in consultation with local stakeholders. In partnership with the latter, demographic, epidemiological, programmatic, as well as cost and spending data for these populations and interventions are then collated. An optimisation analysis of TB spending was conducted in Belarus, using program objectives and constraints defined in collaboration with local stakeholders, which included experts, decision makers, funders and organisations involved in service delivery, support and technical assistance. These analyses show that it is possible to improve health impact by redistributing current TB spending in Belarus. Specifically, shifting funding from inpatient- to outpatient-focused care models, and from mass screening to active case finding strategies, could reduce TB prevalence and mortality by up to 45% and 50%, respectively, by 2035. In addition, an optimised allocation of TB spending could lead to a reduction in drug-resistant TB infections by 40% over this period. This would support progress towards national TB targets without additional financial resources. The case study in Belarus demonstrates how reallocations of spending across existing and new interventions could have a substantial impact on TB outcomes. This highlights the potential for Optima TB and similar modelling tools to support evidence-based priority setting., Author summary Tuberculosis (TB) remains a leading global cause of death and morbidity, and 85% of deaths occur in countries where resources for TB care and control are limited. Many countries cannot finance all TB interventions or technologies, which means difficult decisions on what to prioritise and publically finance. Modelling tools can help decision-makers set priorities based on evidence, in a systematic and transparent way. This study presents Optima TB, a tool that estimates which allocations of spending across interventions will most likely maximise specified objectives—such as minimising TB deaths, prevalence and incidence. In partnership with local decision-makers and stakeholders, Optima TB was applied in Belarus. Recommendations from the model findings include focussing investment on outpatient rather than inpatient care and actively finding people with TB (e.g. through contact tracing) rather than mass testing of the population. The recommended reallocations of spending could reduce TB prevalence and deaths by up to 45% and 50%, respectively, by 2035 for the same amount of spending. Key stakeholders were engaged throughout the analysis and findings and uncertainty around the results were clearly communicated with decision-makers. The timeliness of the results helped inform national dialogue on TB care reform, among other key policy discussions.
- Published
- 2021
49. Predicting seasonal influenza using supermarket retail records
- Author
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Giulio Rossetti, Salvatore Rinzivillo, Alessandro Vespignani, Ioanna Miliou, Qian Zhang, Dino Pedreschi, Fosca Giannotti, Xinyue Xiong, Miliou, I., Xiong, X., Rinzivillo, S., Zhang, Q., Rossetti, G., Giannotti, F., Pedreschi, D., and Vespignani, A.
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FOS: Computer and information sciences ,RNA viruses ,Computer Science - Machine Learning ,Viral Diseases ,020205 medical informatics ,Nowcasting ,Economics ,Epidemiology ,Computer science ,Social Sciences ,02 engineering and technology ,medicine.disease_cause ,Geographical locations ,Proxy (climate) ,Machine Learning (cs.LG) ,Machine Learning ,Seasonal influenza ,Medical Conditions ,Mathematical and Statistical Techniques ,Medicine and Health Sciences ,0202 electrical engineering, electronic engineering, information engineering ,Econometrics ,Influenza A virus ,Biology (General) ,Supermarkets ,health care economics and organizations ,Pathology and laboratory medicine ,0303 health sciences ,education.field_of_study ,Settore INF/01 - Informatica ,Ecology ,Incidence ,Statistics ,Commerce ,Computer Science - Social and Information Networks ,Medical microbiology ,Europe ,Infectious Diseases ,Italy ,Computational Theory and Mathematics ,Autoregressive model ,Computational Biology ,Consumer Behavior ,Humans ,Influenza, Human ,Seasons ,Modeling and Simulation ,Physical Sciences ,Viruses ,Pathogens ,Human ,Research Article ,Computer and Information Sciences ,Time series ,Infectious Disease Control ,QH301-705.5 ,Computer Science - Artificial Intelligence ,Population ,Disease Surveillance ,Research and Analysis Methods ,Microbiology ,03 medical and health sciences ,Cellular and Molecular Neuroscience ,Artificial Intelligence ,Genetics ,medicine ,Influenza viruses ,European Union ,Statistical Methods ,education ,Molecular Biology ,Ecology, Evolution, Behavior and Systematics ,030304 developmental biology ,Social and Information Networks (cs.SI) ,Biology and life sciences ,Retail ,Organisms ,Viral pathogens ,Influenza ,Microbial pathogens ,Support vector machine ,Artificial Intelligence (cs.AI) ,Infectious Disease Surveillance ,Season ,People and places ,Mathematics ,Forecasting ,Orthomyxoviruses - Abstract
Increased availability of epidemiological data, novel digital data streams, and the rise of powerful machine learning approaches have generated a surge of research activity on real-time epidemic forecast systems. In this paper, we propose the use of a novel data source, namely retail market data to improve seasonal influenza forecasting. Specifically, we consider supermarket retail data as a proxy signal for influenza, through the identification of sentinel baskets, i.e., products bought together by a population of selected customers. We develop a nowcasting and forecasting framework that provides estimates for influenza incidence in Italy up to 4 weeks ahead. We make use of the Support Vector Regression (SVR) model to produce the predictions of seasonal flu incidence. Our predictions outperform both a baseline autoregressive model and a second baseline based on product purchases. The results show quantitatively the value of incorporating retail market data in forecasting models, acting as a proxy that can be used for the real-time analysis of epidemics., Comment: 17 pages, 2 figures, 4 tables (1 in appendix), 1 algorithm, submitted to PLOS Computational Biology
- Published
- 2021
50. Estimating Costs and Benefits of CTL Escape Mutations in SIV/HIV Infection.
- Author
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Ganusov, Vitaly V. and De Boer, Rob J.
- Subjects
GENETIC mutation ,MICROBIAL mutation ,MEDICAL care costs ,T cell receptors ,LYMPHOCYTES ,HIV infections ,SIMIAN viruses ,PREVENTION ,ECONOMICS - Abstract
Mutations that allow SIV/HIV to avoid the cytotoxic T lymphocyte (CTL) response are well documented. Recently, there have been a few attempts at estimating the costs of CTL escape mutations in terms of the reduction in viral fitness and the killing rate at which the CTL response specific to one viral epitope clears virus-infected cells. Using a mathematical model we show that estimation of both parameters depends critically on the underlying changes in the replication rate of the virus and the changes in the killing rate over time (which in previous studies were assumed to be constant). We provide a theoretical basis for estimation of these parameters using in vivo data. In particular, we show that 1) by assuming unlimited virus growth one can obtain a minimal estimate of the fitness cost of the escape mutation, and 2) by assuming no virus growth during the escape, one can obtain a minimal estimate of the average killing rate. We also discuss the conditions under which better estimates of the average killing rate can be obtained. [ABSTRACT FROM AUTHOR]
- Published
- 2006
- Full Text
- View/download PDF
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